I recently filed forms for Social Security and Medicare to the IRS(4 weeks ago), to be reimbursed as my employer had withheld the money in error. This morning I received a letter from the IRS stating that they haven't resolved the matter because they haven't completed all the research necessary for a complete response. I am on a J-1 visa as an exchange visitor (teacher) with a Malawi citizenship. I am trying to claim back the money that was withheld in error in the past 2 years. The IRS says they will contact me in the next 45 days. Is there a problem? Will I get my money back or are they hoping I will not pursue the request? What should I do?

When did you enter the U.S.
Malawi does not have any tax treaty with the U.S. so on your income you must pay income taxes. Every one on J1 is exempt from FICA taxes (social security and Medicare) for 2 years.
Read about FICA taxes: Your U.S. Tax Return: Social Security and Medicare (FICA) Taxes for Non-resident Exempt Individual

Yes, IRS takes 8 to 12 weeks to process your FICA refund form. You must wait.

I entered the USA August 23rd, 2006.

There is probably no problem.

Like the letter said, it is just taking longer than expected to process your refund request.

Please be patient.

BTW, you become liabel for FICA (Social Security and Medicare) taxes on 1 January 2008. You should make sure your employer is aware of that fact.